Question: ChAMP ComBat step error: Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
0
gravatar for Daniel E. Weeks
3.3 years ago by
Pittsburgh, Pennsylvania, United States of America
Daniel E. Weeks0 wrote:

When trying to run ChAMP version 1.8.2 on a data set of 91 samples using the default champ.process command, it got through the SVD step, but then died at the ComBat step:

Preparing files for ComBat
Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
Calls: champ.process -> champ.runCombat
In addition: Warning messages:
1: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
2: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
3: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
4: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
5: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
6: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
Execution halted

 

In champ.norm, I see code like this:

if (min(beta.p, na.rm = TRUE) == 0) {

but in champ.runCombat, I see this (which lacks the na.rm option):

if (min(beta.c) == 0) {

I am not sure how to debug this.  

Thank you.

 

 

 

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Daniel E. Weeks0
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